Oct 2026· Zenodo (CERN European Organization for Nuclear Research)
Protein Structure and Dynamics
Abstract
Code accompanying the paper "Ancient amino acid sets enable stable protein folds" (Giacobelli, Andersson, et al., bioRxiv 2025, doi:10.1101/2025.10.29.685319). Contents: Protein design pipeline: RFdiffusion backbones, ProteinMPNN sequences restricted to a 10-amino-acid ancient alphabet, and a 20-amino-acid comparison design Structural analysis of the designs (TM-score, RMSD, DSSP, ESMFold) Mutational robustness simulations (10 vs 20 amino acids), with the raw results and statistics from the paper Install with uv sync. External tools (RFdiffusion, ProteinMPNN, US-align) are installed separately; see the README. Licence: MIT. To cite, see CITATION.cff.
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